However, assembly was more common back then and really wasn't consider a 'black art'. It was just what you did. Also, 8 bits were a lot simpler to program (flat address space, no protected mode, etc) - at most, you might have to deal with some bank switching..
Even hobbyist mags like Compute! would run articles on assembly - and DDJ would have that fancy 'C' stuff too!
You could read the entire OS ("KERNAL") and BASIC disassembly start to finish (there were books listing them, with comments added). You could systematically test what changing registers would do - I remember pestering my parents at work by calling them to let them hear what sounds I managed to make by randomly POKE'ing things into the sound registers just to experiment.
And of course the manuals. While I agree with you books were hard to get, the C64 manual was fantastic.
To GGP: you should get an 8-bit computer and play around a bit, some things may blow your mind. I first played around with a C64 in around 7th grade, after I'd already learned some programming on PCs, and I learned a lot.